A more sustainable use of plant protection products (PPPs) is promoted by European Union governments. Indeed, each country is encouraging the development of complements and alternatives to chemical PPPs in order to reduce their use. From this initiative, PPPs from natural sources are promoted, namely biocontrol products (BPs). These new BPs are complex mixtures or microbial strains that are difficult to monitor in complex environmental matrices. Besides, they present modes of action that are not fully understood. More knowledge is therefore needed to better use and regulate these BPs. Thus, this thesis focuses on (1): the investigation of BPs fate on treated plants through a kinetics study monitoring their residues and (2): the plant response to the treatment; in order to better understand the mechanisms involved in BPs efficacy and how they interact with the plant and the environment. Firstly, a new tool was developed in order to study residues fate. It is based on an innovative approach (Environmental Metabolic Footprinting, EMF) that was optimized during the thesis in order (1): to be adapted to fruit matrix (peach peels) and (2): to target only the xenometabolome (residues fate). Secondly, plant response to two BPs treatments at transcripts and metabolites levels was evaluated. RNA sequencing gave data about the different genes expression following treatments with BPs compared to the untreated controls. These data were completed with metabolic analysis (phytohormones, phenols, and organic acids). Strong hints were found on grapevine defense induction by the treatments, but further investigations are necessary in order to confirm these first results.